Malaria remains a leading cause of underfive morbidity and mortality in sub-Saharan Africa. Effective case management is a strategy recommended by the World Health Organization for its control. A clinical audit of case management of uncomplicated malaria in underfives in health facilities in Cross River State, Nigeria, was conducted from January to March 2012. Data was extracted from patients’ case records by trained medical personnel using pretested data extraction forms. Of the 463 case records reviewed, age, gender, and weight were reported in 98.1%, 97.3%, and 49.7% of the children, respectively. A history of fever was obtained in 89.6% and a record of temperature in 74.1% of the children. General examination was performed in 203 (43.8%) children. Malaria parasite test was requested in 132 (28.5%) while Packed cell volume or haemoglobin was requested in 107 (23.1%) children. Appropriate dose of Artemisinin Combination Therapy (ACT) was instituted in 300 (64.8%), wrong dose in 109 (23.5%), and inappropriate treatment in 41 (8.9%). The utilization of ACTs for treating uncomplicated malaria in the State has improved but clinical assessment of patients and laboratory confirmation of diagnosis are suboptimum.